Nature Protocols最新文献

{"title":"A general approach for the synthesis of nanoisland catalysts.","authors":"Xu Li, Di Wu, Jingyi Zhang, Yuan Ji, Junyi He, Chuan Xia","doi":"10.1038/s41596-026-01431-0","DOIUrl":"https://doi.org/10.1038/s41596-026-01431-0","url":null,"abstract":"<p><p>The stabilization of metal catalysts remains a major challenge in heterogeneous catalysis, particularly for single atoms and clusters that operate under demanding industrial conditions where sintering and agglomeration often lead to substantial deactivation. Here, to address the issue, this protocol presents a general method for synthesizing nanoisland catalysts in which nanoscale oxide islands are isolated on high-surface-area substrates to confine and stabilize metal species. The method uses strong electrostatic adsorption to deposit oxides such as CeO_x, LaO_x and InO_x onto substrates such as SiO₂ and Al₂O₃, resulting in small-sized, high-density and uniformly distributed nanoislands. Then, transition-metal precursors, including those of Pt, Pd and Ru, are introduced in a controlled manner such that single atoms or clusters are positioned preferentially on the nanoislands. These nanoislands have stronger interactions with metals than the substrates do, confining metal species within well-defined regions and preventing their migration and agglomeration. This confinement effect is crucial for maintaining the dispersion and activity of metal catalysts, especially at elevated temperatures. Compared with conventional impregnation or deposition-precipitation methods, this approach achieves more precise spatial control over metal deposition and creates strong confinement environments that effectively suppress sintering. This protocol enables the preparation of thermally stable small-sized metal catalysts suitable for fuel processing, exhaust treatment, chemical manufacturing and other uses. The complete workflow, which includes oxide deposition, metal loading and material characterization, typically requires about 4 d, and catalytic testing requires an additional 5-20 h depending on the system. The protocol can be implemented in laboratories equipped with standard wet-chemistry facilities and with prior experience in synthesizing inorganic nanomaterials.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148679557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reply to: Overestimations in the cyclization efficiency of small, restriction enzyme-digested DNA fragments.","authors":"Roman Teo Oliynyk, George M Church","doi":"10.1038/s41596-026-01424-z","DOIUrl":"https://doi.org/10.1038/s41596-026-01424-z","url":null,"abstract":"","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overestimations in the cyclization efficiency of small, restriction enzyme-digested DNA fragments.","authors":"Fenfei Leng","doi":"10.1038/s41596-026-01423-0","DOIUrl":"10.1038/s41596-026-01423-0","url":null,"abstract":"","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Core2Edge: a human glioblastoma organoid-brain slice model capturing infiltration and transcriptional heterogeneity from core to single-cell dispersion.","authors":"Ahmad Melhem, Barbara E F Pregler, Juan Eduardo Rodriguez-Gatica, Lea L Friker, Jake Thomas, Marieta I Toma, Mike-Andrew Westhoff, Vidhya M Ravi, Valeri Borger, Dieter Henrik Heiland, Julian P Layer, Andreas Schlitzer, Torsten Pietsch, Michael Hölzel, Andreas Waha, Hartmut Vatter, Martin K Schwarz, Ulrich Herrlinger, Ulrich Kubitscheck, Anna-Laura Potthoff, Matthias Schneider","doi":"10.1038/s41596-026-01412-3","DOIUrl":"https://doi.org/10.1038/s41596-026-01412-3","url":null,"abstract":"<p><p>Glioblastomas function as intricate cellular networks that extend into the surrounding brain tissue, facilitating long-distance communication. This malignant connectivity spans from the tumor core to remote infiltration zones, in support of the concept of glioblastoma as a whole-brain disease. With growing ethical concerns in biomedical research and the inherent limitations of animal models in recapitulating human glioblastoma biology, there is an increasing demand for human ex vivo platforms capable of capturing the full infiltration spectrum from the tumor core to single-cell dispersion. Here we present a 3D, fully human ex vivo glioblastoma model (Core2Edge) that replicates this extensive infiltration range while preserving the intratumoral heterogeneity of the original tumor. This model involves implanting fluorescently labeled human glioblastoma organoids (GBOs) into organotypic human brain slices, maintaining the genetic integrity and cytoarchitecture of both brain and tumor. By combining tissue expansion with light-sheet fluorescence microscopy, we achieve high-resolution, 3D imaging of the entire GBO-brain slice model. This approach allows the study of initial infiltration steps, in-depth analysis of the invasive front, and exploration of cell-cell interactions between tumor cells and the tumor microenvironment, and offers a platform for drug screening and testing, reducing the need for animal models. Once GBOs are prepared, the protocol takes ~7-12 d. Key steps include brain slice preparation (~4-6 h, depending on quantity), 1 d for initial culture before GBO staining and transplantation, a variable culture period (≤10 d), and fixation (~8 h). The protocol requires experience with human brain slice and organoid culture.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Three-dimensional tracking of dynamic structures in living cells using single-plane imaging with focus feedback.","authors":"Simona V Antonova, Wim Pomp, Joseph V W Meeussen, Tineke L Lenstra","doi":"10.1038/s41596-026-01419-w","DOIUrl":"https://doi.org/10.1038/s41596-026-01419-w","url":null,"abstract":"<p><p>Tracking dynamic subcellular processes in live cells presents a major challenge in biological research, as it often requires high precision in three-dimensional imaging. Here this protocol introduces a focus-feedback microscopy algorithm that enables the accurate tracking of structures within a single optical plane over time, thereby overcoming the limitations of traditional z-stack imaging and reducing imaging intervals and light exposure. This results in prolonged imaging sessions with minimal phototoxicity, making it ideal for studying dynamic molecular processes in living cells. The protocol provides step-by-step guidance for integrating the focus-feedback algorithm within Zeiss Zen or custom microscope software, incorporating cylindrical lenses for z-position detection, performing bead-based calibration and analyzing time-lapse data using both standard and custom tools. It is designed to be accessible to researchers with varying levels of experience and, depending on research question, can be completed within a single day. Focus-feedback microscopy has been successfully applied to track single gene loci within the nucleus and has potential extensions to cytoplasmic structures such as organelles or vesicles. Its compatibility with multichannel and single-molecule imaging makes it a powerful tool for studying dynamic cellular processes with precise spatial and temporal resolution.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A programmable DNA tetrahedron platform for selective and efficient capture of cells and proteins.","authors":"Xingyu Chen, Wumeng Yin, Songhang Li, Xiaoxiao Cai, Yunfeng Lin, Taoran Tian","doi":"10.1038/s41596-026-01410-5","DOIUrl":"https://doi.org/10.1038/s41596-026-01410-5","url":null,"abstract":"<p><p>The selective capture of endogenous cells and proteins holds immense potential in regenerative medicine, single-cell analysis, biosensing and cell therapy. However, conventional multivalent platforms suffer from uncontrolled ligand distribution and poor spatial alignment, limiting capture efficiency. Here we provide a protocol for a programmable tetrahedral DNA nanostructure (TDN) platform that enables precise spatial control of capture ligands through site-specific editability. This protocol describes two distinct capture systems: (1) an aptamer-functionalized TDN for the selective capture of mesenchymal stem cells, which increases binding affinity 2.25-fold and achieves ~90% capture efficiency, and (2) a peptide-functionalized TDN-hydrogel for sequestering endogenous growth factors, which enhances capture efficiency from <40% with conventional methods to nearly 90%. The complete protocol, from computational design and nanostructure assembly to in vitro functional validation, can be completed in ~10-20 d, with subsequent in vivo studies extending over several weeks. This versatile platform enables the rational design of high-efficiency capture agents for diverse biological targets, providing a powerful and adaptable tool for tissue engineering, cell sorting and biosensing.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive quantitative analysis of polyolefin hydrogenolysis toward plastic waste management.","authors":"Chao Meng, Yi-Yu Wang, Xun Wu, Akalanka Tennakoon, Anne M LaPointe, Frédéric A Perras, Long Qi, Baron G Peters, Aaron D Sadow, Wenyu Huang","doi":"10.1038/s41596-026-01385-3","DOIUrl":"https://doi.org/10.1038/s41596-026-01385-3","url":null,"abstract":"<p><p>New methods for recovering the energy and value from polyolefin plastic waste must account for all the hydrocarbons formed during a deconstruction reaction. Analysis of the reaction mixture distribution is key to determining a catalyst's performance (activity and selectivity) and evaluating the economic viability of a conversion process. The molecular species present in the reaction mixtures can range from H₂ and CH₄ to hyper-branched hydrocarbons above 100,000 g/mol and any hydrocarbon in between; therefore, multiple analytical techniques are required to quantify all of the products. Here we describe an optimized and validated workflow that uses integrated analytical gas chromatography for concurrent H₂ and gas-phase hydrocarbon quantification of the headspace; complementary gas chromatography, liquid chromatography and multi-nuclear magnetic resonance spectroscopy to quantify the composition of soluble products, as well as gel permeation chromatography to determine of the molecular weight distribution of the residual insoluble polymeric material. Using polyolefin hydrogenolysis in an autoclave reactor as an example, we describe how to specifically adapt these techniques to polymer deconstruction experiments and fully quantify the entire hydrocarbon population, while resolving and assigning specific species and characterizing structures. The information from this comprehensive analysis is needed to study reaction kinetics and to evaluate the intrinsic activity of a catalyst and reactivity of polymers in upcycling experiments, enabling mechanistic investigations and providing data to link experiment and theoretical models. The comprehensive quantitative analysis in this protocol can be completed within 4 d.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148584773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tutorial: guidance on the use of large language models for medical research.","authors":"Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu","doi":"10.1038/s41596-026-01408-z","DOIUrl":"10.1038/s41596-026-01408-z","url":null,"abstract":"<p><p>Frontier large language models (LLMs), such as GPT-5, Claude 4.5, Gemini 3, Llama 4 and DeepSeek-R1, represent a transformative class of artificial intelligence tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials and answering medical questions. Here in this Tutorial, we discuss an actionable set of best practices to help healthcare professionals utilize LLMs more effectively and efficiently. The overall workflow follows sequential phases from formulating the task, choosing the most appropriate LLMs, engineering the prompts, fine-tuning the requests and through to model deployment. We discuss a set of critical considerations in identifying medical tasks that align with the core capabilities of LLMs and selecting models based on the required task, data, performance and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. We then cover deployment considerations, including regulatory compliance, ethical guidelines and continuous monitoring for fairness and bias. By providing a structured step-by-step methodology, this entry-level tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13454964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148584782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formulation and activation of lipid-shelled nanobubble ultrasound contrast agents.","authors":"Michaela B Cooley, Theresa Kosmides, Pinunta Nittayacharn, Felipe M Berg, Dana Wegierak, Dorian Durig, Agata A Exner","doi":"10.1038/s41596-026-01411-4","DOIUrl":"https://doi.org/10.1038/s41596-026-01411-4","url":null,"abstract":"<p><p>Ultrasound is the second most common clinical imaging modality. Ultrasound image quality often suffers from poor contrast resolution and thus can greatly benefit from appropriate contrast agents. While micron-sized gas core particles (microbubbles) are clinically utilized in this space for applications such as echocardiography, a smaller agent could be more broadly applicable to enhance the sensitivity and specificity of disease detection. To this end, lipid-shelled nanobubbles have recently emerged as robust ultrasound contrast agents for both diagnostic and therapeutic purposes. They have been used in preclinical applications ranging from oncology to endocrinology and are notably relevant in diseases that involve pathological vasculature. Owing to their shell composition, nanobubbles are versatile and can be functionalized with fluorophores, targeting agents and therapeutic moieties. Here we provide the steps needed to formulate plain, fluorophore-conjugated, ligand-conjugated, hydrophilic dye-integrated and drug-loaded nanobubbles. The typical formulation for lipid-shelled nanobubbles takes place via self-assembly driven by mechanical agitation, followed by differential centrifugation. The process is deceptively simple, yet there are many nuances in the formulation process that must be followed to produce consistently successful nanobubble batches without contamination from microbubbles. Even minor deviation from the standard protocol can substantially affect nanobubble yield, stability, acoustic performance and batch-to-batch reproducibility. This procedure also details common pitfalls and their potential consequences for bubble quality and performance. The procedure requires 3 h to complete the formulation and activation of the plain nanobubbles by users with basic laboratory expertise.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying lipid-protein interactomes with functional lipid probes.","authors":"Scotland E Farley, Gaelen Guzman, Berit Blume, Per Haberkant, Carsten Schultz, Fikadu G Tafesse","doi":"10.1038/s41596-026-01405-2","DOIUrl":"https://doi.org/10.1038/s41596-026-01405-2","url":null,"abstract":"<p><p>Cellular lipids shape health and disease through specific protein interactions, yet lipid-protein networks remain poorly defined. Despite rapid advances in functional lipid probes, the field still lacks a practical, dedicated protocol for conducting lipid-protein interaction studies. We describe detailed methods for determining lipid interactomes within cells using multifunctionalized lipid derivatives. We provide a protocol that details how to (i) treat cells with lipid derivatives and perform photochemistry to obtain lipid-protein conjugates, (ii) extract cellular lysates for downstream analysis, (iii) perform click chemistry on lysates with a fluorophore and observe lipid-protein conjugates by in-gel fluorescence and (iv) perform click chemistry on lysates with azide beads and prepare lipid-protein conjugates for proteomic analysis. We provide context on important parameters for each step and include guidelines for controls, as well as suggestions for troubleshooting based on common problems encountered during the preparation of this protocol. This protocol enables identification of proteins that bind to specific lipids across diverse biological systems and cellular states. The entire workflow from cell treatment to complete proteomic sample preparation requires ~15 h over 4 d, depending on the type of experimental readout (in-gel fluorescence or proteomics) and the usage of pause points. Practitioners are expected to be familiar with standard biochemical techniques, such as sterile sample handling and tissue culture and gel electrophoresis. Additional skills are needed for mass spectrometric analysis, and collaboration with a proteomics core facility is recommended. The described procedures uniquely enable the identification of the protein interactors (the interactome) of select lipid species, providing for a major advance in the characterization of the biological roles of lipids in cellular systems.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}